PEX19 p.Lys245=
c.735G>A · rs749331745 · VCV1158078
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.025%, amr)
Conditions
1
peroxisome biogenesis disorder 12A (Zellweger)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.121 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.62 | GERP 0.46, phastCons 0.99 |
| Overall | ||
| CADD | 8.539 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.025%
Admixed American · 15/59,996 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0124%
Overall
0.000929%
15/1,613,826 alleles · ultra-rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PEX19
- Protein
- p.Lys245=
- Coding
- c.735G>A
- MANE Select
- NM_002857
- dbSNP
- rs749331745
- Type
- single nucleotide variant
- Location
- chr1:160280106 (GRCh38)
- Gene constraint
- LOEUF 1.066 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.95 · 5 PDB
- Residue 245
- an α-helix
Similar variants
- PEX19 c.346+2T>C Likely pathogenic ★★ same condition
- PEX19 p.Leu94Ter Likely pathogenic ★★ same condition
- PEX19 p.Lys193Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX19 p.Ser54Leu Pathogenic ★★ ⚠ same condition
- PEX19 c.*1335G>T Uncertain significance ★★ same condition
- PEX19 c.*864C>T Uncertain significance ★★ same condition
- PEX19 p.Ala14Pro Uncertain significance ★★ ⚠ same condition
- PEX19 p.Ala234Ser Uncertain significance ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/pex19-p-lys245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown